The Department of Health requested that Nestle withdraw Lactogen 1 and Nido 1+ with immediate effect.
Nido 1+ is designed to aid digestion in toddlers. Products with serial code 81790181SO2E1M 900g have been recalled.
Thousands of babies in China fell ill recently after drinking formula containing melamine. At least four died.
Nestle has however emphasised that the products "are absolutely safe for consumption", but said the company is co-operating with the health department in recalling the batch.
"In the absence of any specific South African legislation for melamine in food, that the traces of melamine detected are more than 10 times lower than the WHO guidance level of health concern," Nestle said.